[gmx-users] number of helical residue

[Justin Lemkul]

On 1/5/13 3:34 PM, Parisa Rahmani wrote:
> Hi gmx users,
>
> I want to get number of helical residue as a function of time ,
> but by running
> g_helix -s protein.tpr -f protein_pbc.pdb -n index.ndx ,
> no n-ahx.xvg output is generated.
>

Looking at the code, no version of Gromacs has ever produced this file.  I have 
removed its reference in the help text for the next release.  Thanks for 
reporting this bug.

You can get a count of any secondary structure element by using do_dssp.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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